What we do not know about sequence analysis and sequence databases

Introduction

The marriage of high-throughput nucleotide sequencing with computational methods for the analysis of nucleotide and protein sequences have ushered in a new era of molecular biology. Entire genomes are deposited into the sequence DBs at a growing rate. Typically, investigators can use computational sequence analysis to assign functions to the majority of the open reading frames in genome sequences. That analysis can identify a surprisingly large fraction of the genes within the organism. That fraction is increasing over time as the sequence databases contain a larger fraction of all functional domains.